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  <div class="section" id="atomman-package">
<h1>atomman package<a class="headerlink" href="#atomman-package" title="Permalink to this headline">¶</a></h1>
<div class="section" id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="atomman.unitconvert.html">unitconvert</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.tools.html">tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.region.html">region</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.cluster.html">cluster</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.mep.html">mep</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.lammps.html">lammps</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.library.html">library</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.defect.html">defect</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.plot.html">plot</a></li>
</ul>
</div>
</div>
<div class="section" id="classes">
<h2>Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="atomman.Atoms.html">Atoms</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.Box.html">Box</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.System.html">System</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.ElasticConstants.html">ElasticConstants</a></li>
<li class="toctree-l1"><a class="reference internal" href="atomman.NeighborList.html">NeighborList</a></li>
</ul>
</div>
</div>
<div class="section" id="module-atomman">
<span id="functions-and-attributes"></span><h2>Functions and attributes<a class="headerlink" href="#module-atomman" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="atomman.build_lammps_potential">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">build_lammps_potential</code><span class="sig-paren">(</span><em class="sig-param">pair_style</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.build_lammps_potential" title="Permalink to this definition">¶</a></dt>
<dd><p>Wrapper function for the PotentialLAMMPSBuilder subclasses.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pair_style</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – The LAMMPS pair_style setting associated with the potential.</p></li>
<li><p><strong>**kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a>) – Any keyword parameters supported by PotentialLAMMPSBuilder and the
subclass that matches the pair_style.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.displacement">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">displacement</code><span class="sig-paren">(</span><em class="sig-param">system_0</em>, <em class="sig-param">system_1</em>, <em class="sig-param">box_reference='final'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.displacement" title="Permalink to this definition">¶</a></dt>
<dd><p>Compute the displacement vectors between all matching atoms for two systems.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>system_0</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – The initial system to calculate displacements from.</p></li>
<li><p><strong>system_1</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – The final system to calculate displacements to.</p></li>
<li><p><strong>box_reference</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.9)"><em>None</em></a>) – Specifies which system’s boundary conditions to use.  ‘initial’ uses
system_0’s box and pbc.  ‘final’ uses system_1’s box and pbc (Default)
None computes the straight difference between the positions without
accounting for periodic boundaries.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The displacement vectors for all atoms.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If the systems have different numbers of atoms or for invalid
    box_reference values.</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.dump">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">dump</code><span class="sig-paren">(</span><em class="sig-param">style</em>, <em class="sig-param">system</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.dump" title="Permalink to this definition">¶</a></dt>
<dd><p>Convert a System to another format.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>style</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – Indicates the format of the content to dump the atomman.System as.</p></li>
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – The system to convert.</p></li>
<li><p><strong>kwargs</strong> (<em>any</em><em>, </em><em>optional</em>) – Any extra keyword arguments to pass to the underlying dump methods.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Any content returned by the underlying dump methods.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)">str</a>, <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)">object</a> or <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)">tuple</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.dump_ase_Atoms">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">dump_ase_Atoms</code><span class="sig-paren">(</span><em class="sig-param">system</em>, <em class="sig-param">symbols=None</em>, <em class="sig-param">return_prop=False</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.dump_ase_Atoms" title="Permalink to this definition">¶</a></dt>
<dd><p>Convert an atomman.System into an ase.Atoms.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – A atomman representation of a system.</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – List of the element symbols that correspond to the atom types.  If not
given, will use system.symbols if set, otherwise no element content
will be included.</p></li>
<li><p><strong>return_prop</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Indicates if the extra per-atom properties are to be returned in a
dictionary.  Default value is False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>aseatoms</strong> (<em>ase.Atoms</em>) – An ase representation of a collection of atoms.</p></li>
<li><p><strong>prop</strong> (<em>dict</em>) – Dictionary containing any extra per-atom properties to include.
Returned if return_prop is True.</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.dump_atom_data">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">dump_atom_data</code><span class="sig-paren">(</span><em class="sig-param">system</em>, <em class="sig-param">f=None</em>, <em class="sig-param">atom_style=None</em>, <em class="sig-param">units=None</em>, <em class="sig-param">natypes=None</em>, <em class="sig-param">potential=None</em>, <em class="sig-param">float_format='%.13f'</em>, <em class="sig-param">return_info=True</em>, <em class="sig-param">prompt=True</em>, <em class="sig-param">comments=True</em>, <em class="sig-param">safecopy=False</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.dump_atom_data" title="Permalink to this definition">¶</a></dt>
<dd><p>Write a LAMMPS-style atom data file from a System.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – The system to write to the atom data file.</p></li>
<li><p><strong>f</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>file-like object</em><em>, </em><em>optional</em>) – File path or file-like object to write the content to.  If not given,
then the content is returned as a str.</p></li>
<li><p><strong>atom_style</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The LAMMPS atom_style option associated with the data file.  If neither
atom_style or potential is given, will set atom_style to ‘atomic’.</p></li>
<li><p><strong>units</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The LAMMPS units option associated with the data file.  If neither
units or potential is given, will set units ‘metal’.</p></li>
<li><p><strong>natypes</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – Allows the natypes value to be manually changed.  This is needed if
natypes needs to be greater than the current number of atypes.  If
neither natypes or potential is given, will use system.natypes.</p></li>
<li><p><strong>potential</strong> (<em>atomman.lammps.Potential</em><em>, </em><em>optional</em>) – Potential-specific values of atom_style, units, and natypes can be
extracted from a Potential object.  If both potential and any of the
individual values are given, the individual values will be used.</p></li>
<li><p><strong>float_format</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – c-style formatting string for floating point values.  Default value is
‘%.13f’.</p></li>
<li><p><strong>return_info</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Indicates if the LAMMPS command lines associated with reading in the
file are to be returned as a str.  If potential is given, then the
commands associated with the potential will be included. Default value
is True.</p></li>
<li><p><strong>prompt</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Used if return_pair_info is True. If prompt is True (default), then a
screen prompt will ask for more details if masses are not unique for
the elements.  If False, an error will be thrown for non-unique masses.</p></li>
<li><p><strong>comments</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Used if return_pair_info is True. If comments is True (default), then
metadata comments associated with the potential will be included in the
pair_info.</p></li>
<li><p><strong>safecopy</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – The LAMMPS data format requires all atoms to be inside box bounds, i.e.
“wrapped”.  If safecopy is True then a copy of the system is made to
keep the original unwrapped.  Default value is False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>content</strong> (<em>str</em>) – The data file contents.  Returned if f is not given.</p></li>
<li><p><strong>read_info</strong> (<em>str</em>) – The LAMMPS input command lines to read the created data file in.
Returned if return_info is True.  If return_pair_info is also True and
potential is given, the LAMMPS input command lines for the potential
are also included.</p></li>
</ul>
</p>
</dd>
<dt class="field-odd">Raises</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If return_pair_info is True and return_info is False or potential is
    not given.</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.dump_atom_dump">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">dump_atom_dump</code><span class="sig-paren">(</span><em class="sig-param">system</em>, <em class="sig-param">f=None</em>, <em class="sig-param">lammps_units='metal'</em>, <em class="sig-param">scale=False</em>, <em class="sig-param">prop_name=None</em>, <em class="sig-param">table_name=None</em>, <em class="sig-param">shape=None</em>, <em class="sig-param">unit=None</em>, <em class="sig-param">dtype=None</em>, <em class="sig-param">prop_info=None</em>, <em class="sig-param">float_format='%.13f'</em>, <em class="sig-param">return_prop_info=False</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.dump_atom_dump" title="Permalink to this definition">¶</a></dt>
<dd><p>Write a LAMMPS-style atom data file from a System.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – The system to write to the atom data file.</p></li>
<li><p><strong>f</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>file-like object</em><em>, </em><em>optional</em>) – File path or file-like object to write the content to.  If not given,
then the content is returned as a str.</p></li>
<li><p><strong>lammps_units</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The LAMMPS units option associated with the table values.  This is used
for the box dimensions and default units for standard dump properties
(not compute/fix definitions).</p></li>
<li><p><strong>scale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Flag indicating if atom positions are to be scaled relative to the box
(True) or given in absolute Cartesian values (False, default).</p></li>
<li><p><strong>prop_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The Atoms properties to include.  If neither prop_name or prop_info are
given, all system properties will be included.</p></li>
<li><p><strong>table_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The dump table column name(s) that correspond to each prop_name.  If not
given, the table_name values will be based on the prop_name and shape
values.</p></li>
<li><p><strong>shape</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The shape of each per-atom property.  If not given, will be inferred
from the length of each table_name value.</p></li>
<li><p><strong>unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – Lists the units for each prop_name as stored in the table.  For a
value of None, no conversion will be performed for that property.  For
a value of ‘scaled’, the corresponding table values will be taken in
box-scaled units.  If not given, unit values will be taken based on
lammps_units if prop_name corresponds to a standard LAMMPS property,
otherwise will be set to None (no conversion).</p></li>
<li><p><strong>dtype</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – Allows for the data type of each property to be explicitly given.
Values of None will infer the data type from the corresponding
property values.  If not given, all values will be None.</p></li>
<li><p><strong>prop_info</strong> (<em>list of dict</em><em>, </em><em>optional</em>) – Structured form of property conversion parameters, in which each
dictionary in the list corresponds to a single atoms property.  Each
dictionary must have a ‘prop_name’ field, and can optionally have
‘table_name’, ‘shape’, ‘unit’, and ‘dtype’ fields.</p></li>
<li><p><strong>float_format</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – c-style formatting string for floating point values.  Default value is
‘%.13f’.</p></li>
<li><p><strong>return_prop_info</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Flag indicating if the filled-in prop_info is to be returned.  Having
this allows for 1:1 load/dump conversions.  Default value is False
(prop_info is not returned).</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>content</strong> (<em>str</em>) – The generated atom_data content.  Only returned if f is None.</p></li>
<li><p><strong>prop_info</strong> (<em>list of dict</em>) – The filled-in prop_info structure. Only returned if
return_prop_info is True.</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.dump_poscar">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">dump_poscar</code><span class="sig-paren">(</span><em class="sig-param">system</em>, <em class="sig-param">f=None</em>, <em class="sig-param">header=''</em>, <em class="sig-param">symbols=None</em>, <em class="sig-param">coordstyle='direct'</em>, <em class="sig-param">box_scale=1.0</em>, <em class="sig-param">float_format='%.13e'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.dump_poscar" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates a poscar-style coordination file for the system.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – The system whose coordinates you are saving</p></li>
<li><p><strong>f</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>file-like object</em><em>, </em><em>optional</em>) – File path or file-like object to write the content to.  If not given,
then the content is returned as a str.</p></li>
<li><p><strong>header</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The comment line to place at the top of the file. Default value is ‘’.</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – List of the element symbols that correspond to the atom types.  If not
given, will use system.symbols if set, otherwise no element content
will be included.</p></li>
<li><p><strong>coordstyle</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The poscar coordinate style to use: ‘cartesian’ or ‘direct’ (i.e.
box relative).  Default value is ‘direct’.</p></li>
<li><p><strong>box_scale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – <dl class="simple">
<dt>A universal scaling constant applied to the box vectors. Default value</dt><dd><p>is 1.0.</p>
</dd>
<dt>float_format<span class="classifier">str, optional</span></dt><dd><p>c-style format for printing the floating point numbers. Default value
is ‘%.13e’.</p>
</dd>
</dl>
</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><strong>poscar_str</strong> – String of the poscar object (only returned if fname is not given).</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)">str</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.dump_pymatgen_Structure">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">dump_pymatgen_Structure</code><span class="sig-paren">(</span><em class="sig-param">system</em>, <em class="sig-param">symbols=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.dump_pymatgen_Structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Convert an atomman.System into a pymatgen.Structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – A atomman representation of a system.</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – List of the element symbols that correspond to the atom types.  If not
given, will use system.symbols if set, otherwise no element content
will be included.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><strong>structure</strong> – A pymatgen representation of a structure.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>pymatgen.Structure</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.dump_system_model">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">dump_system_model</code><span class="sig-paren">(</span><em class="sig-param">system</em>, <em class="sig-param">f=None</em>, <em class="sig-param">box_unit=None</em>, <em class="sig-param">prop_name=None</em>, <em class="sig-param">unit=None</em>, <em class="sig-param">prop_unit=None</em>, <em class="sig-param">format=None</em>, <em class="sig-param">indent=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.dump_system_model" title="Permalink to this definition">¶</a></dt>
<dd><p>Dumps a JSON/XML System.model() representation of the system.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – The system to generate the data model for.</p></li>
<li><p><strong>f</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>file-like object</em><em>, </em><em>optional</em>) – File path or file-like object to write the content to.  If not given,
then the content is returned as a DataModelDict.</p></li>
<li><p><strong>box_unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – Length unit to use for the box. Default value is ‘angstrom’.</p></li>
<li><p><strong>prop_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The Atoms properties to include.  If neither prop_name nor prop_unit
are given, all system properties will be included.</p></li>
<li><p><strong>unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – Lists the units for each prop_name as stored in the table.  For a
value of None, no conversion will be performed for that property.  For
a value of ‘scaled’, the corresponding table values will be taken in
box-scaled units.  If neither unit nor prop_units given, pos will be
given in Angstroms and all other values will not be converted.</p></li>
<li><p><strong>prop_unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a><em>, </em><em>optional</em>) – dictionary where the keys are the property keys to include, and
the values are units to use. If neither unit nor prop_units given,
pos will be given in Angstroms and all other values will not be
converted.</p></li>
<li><p><strong>format</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – File format ‘xml’ or ‘json’ to save the content as if f is given.  If
f is a filename, then the format will be automatically inferred from
f’s extension.  If format is not given and cannot be inferred, then it
will be set to ‘json’.</p></li>
<li><p><strong>indent</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.9)"><em>None</em></a><em>, </em><em>optional</em>) – Indentation option to use for XML/JSON content if f is given.  A value
of None (default) will add no line separatations or indentations.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><strong>model</strong> – The generated model representation of the system.  Will be a
DataModelDict if format is not specified, and a JSON- or XML-formatted
string if format is specified.  Returned if f is not given.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>DataModelDict.DataModelDict or <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)">str</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.dump_table">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">dump_table</code><span class="sig-paren">(</span><em class="sig-param">system</em>, <em class="sig-param">f=None</em>, <em class="sig-param">prop_name=None</em>, <em class="sig-param">table_name=None</em>, <em class="sig-param">shape=None</em>, <em class="sig-param">unit=None</em>, <em class="sig-param">dtype=None</em>, <em class="sig-param">prop_info=None</em>, <em class="sig-param">header=False</em>, <em class="sig-param">float_format='%.13f'</em>, <em class="sig-param">return_prop_info=False</em>, <em class="sig-param">extra=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.dump_table" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts a system’s atoms’ values to a string table.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – An atomman representation of a system.</p></li>
<li><p><strong>f</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>file-like object</em><em>, </em><em>optional</em>) – File path or file-like object to write the content to.  If not given,
then the content is returned as a str.</p></li>
<li><p><strong>prop_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The Atoms properties to include.  Must be given if prop_info is not.</p></li>
<li><p><strong>table_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The table column name(s) that correspond to each prop_name.  If not
given, the table_name values will be based on the prop_name values.</p></li>
<li><p><strong>shape</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The shape of each per-atom property.  If not given, will be inferred
from the length of each table_name value.</p></li>
<li><p><strong>unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – Lists the units for each prop_name as stored in the table.  For a
value of None, no conversion will be performed for that property.  For
a value of ‘scaled’, the corresponding table values will be taken in
box-scaled units.  If not given, all unit values will be set to None
(i.e. no conversions).</p></li>
<li><p><strong>dtype</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – Allows for the data type of each property to be explicitly given.
Values of None will infer the data type from the corresponding
property values.  If not given, all values will be None.</p></li>
<li><p><strong>prop_info</strong> (<em>list of dict</em><em>, </em><em>optional</em>) – Structured form of property conversion parameters, in which each
dictionary in the list corresponds to a single atoms property.  Each
dictionary must have a ‘prop_name’ field, and can optionally have
‘table_name’, ‘shape’, ‘unit’, and ‘dtype’ fields.</p></li>
<li><p><strong>header</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Flag indicating whether to include the column names in the outputted
table.  Default value is False (no column names).</p></li>
<li><p><strong>float_format</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – c-style formatting string for floating point values.  Default value is
‘%.13f’.</p></li>
<li><p><strong>return_prop_info</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Flag indicating if the filled-in prop_info is to be returned.  Having
this allows for 1:1 load/dump conversions.  Default value is False
(prop_info is not returned).</p></li>
<li><p><strong>extra</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a><em>, </em><em>optional</em>) – Allows extra per-atom data that is not part of the System to be
included in the generated table.  Useful when the per-atom data only
has meaning in the tabular format and should not be added to System.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The generated data table.  Only returned if fp is None.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)">str</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.dmag">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">dmag</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomman.dmag" title="Permalink to this definition">¶</a></dt>
<dd><p>Computes the shortest distance between pos_0 and pos_1 using box
dimensions and accounting for periodic boundaries.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pos_0</strong> (<em>numpy.ndarray</em><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a>) – Absolute Cartesian vector position(s) to use as reference point(s).</p></li>
<li><p><strong>pos_1</strong> (<em>numpy.ndarray</em><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a>) – Absolute Cartesian vector position(s) to find relative to pos_0.</p></li>
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – Defines the system/box dimensions</p></li>
<li><p><strong>pbc</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, or </em><em>numpy.ndarray of bool.</em>) – Three Boolean values indicating which of the three box vectors are
periodic (True means periodic).</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The shortest vector magnitude from each pos_0 to pos_1 positions.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.dvect">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">dvect</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomman.dvect" title="Permalink to this definition">¶</a></dt>
<dd><p>Computes the shortest vector between pos_0 and pos_1 using box
dimensions and accounting for periodic boundaries.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pos_0</strong> (<em>numpy.ndarray</em><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a>) – Absolute Cartesian vector position(s) to use as reference point(s).</p></li>
<li><p><strong>pos_1</strong> (<em>numpy.ndarray</em><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a>) – Absolute Cartesian vector position(s) to find relative to pos_0.</p></li>
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – Defines the system/box dimensions</p></li>
<li><p><strong>pbc</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, or </em><em>numpy.ndarray of bool.</em>) – Three Boolean values indicating which of the three box vectors are
periodic (True means periodic).</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The shortest vectors from each pos_0 to pos_1 positions.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.load">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">load</code><span class="sig-paren">(</span><em class="sig-param">style</em>, <em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.load" title="Permalink to this definition">¶</a></dt>
<dd><p>Load a System.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>style</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – Indicates the format of the content to load as an atomman.System</p></li>
<li><p><strong>args</strong> – Any positional-dependent arguments to pass to the underlying load methods.</p></li>
<li><p><strong>kwargs</strong> – Any keyword arguments to pass to the underlying load methods.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><strong>system</strong> – The system object associated with the data model.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.load_ase_Atoms">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">load_ase_Atoms</code><span class="sig-paren">(</span><em class="sig-param">aseatoms</em>, <em class="sig-param">symbols=None</em>, <em class="sig-param">prop={}</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.load_ase_Atoms" title="Permalink to this definition">¶</a></dt>
<dd><p>Convert an ase.Atoms into an atomman.System.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>aseatoms</strong> (<em>ase.Atoms</em>) – An ase representation of a collection of atoms.</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – Allows the list of element symbols to be assigned during loading.
Useful if the symbols for the model differ from the standard element
tags.</p></li>
<li><p><strong>prop</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a><em>, </em><em>optional</em>) – Dictionary containing any extra per-atom properties to include.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><strong>system</strong> – A atomman representation of a system.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.load_atom_data">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">load_atom_data</code><span class="sig-paren">(</span><em class="sig-param">data</em>, <em class="sig-param">pbc=(True</em>, <em class="sig-param">True</em>, <em class="sig-param">True)</em>, <em class="sig-param">symbols=None</em>, <em class="sig-param">atom_style=None</em>, <em class="sig-param">units='metal'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.load_atom_data" title="Permalink to this definition">¶</a></dt>
<dd><p>Read a LAMMPS-style atom data file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>file-like object</em>) – The atom data content to read.  Can be str content, path name, or open
file-like object.</p></li>
<li><p><strong>pbc</strong> (<em>list of bool</em>) – Three boolean values indicating which System directions are periodic.
Default value is (True, True, True).</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – Allows the list of element symbols to be assigned during loading.</p></li>
<li><p><strong>atom_style</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The LAMMPS atom_style option associated with the data file.  Optional
as the data can list this value in a comment in the Atoms section
header.  If not given and not found in data, the default value of
‘atomic’ is used.</p></li>
<li><p><strong>units</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The LAMMPS units option associated with the data file.  Default value
is ‘metal’.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The corresponding system.  Note all property values will be
automatically converted to atomman.unitconvert’s working units.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><ul class="simple">
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#FileNotFoundError" title="(in Python v3.9)"><strong>FileNotFoundError</strong></a> – If data is (likely) a file name and no matching file is found.</p></li>
<li><p><strong>FileFormatError</strong> – If required content fields not found.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If atom_style is both given as a parameter and found in data, but are
    not the same</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.load_atom_dump">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">load_atom_dump</code><span class="sig-paren">(</span><em class="sig-param">data</em>, <em class="sig-param">symbols=None</em>, <em class="sig-param">lammps_units='metal'</em>, <em class="sig-param">prop_name=None</em>, <em class="sig-param">table_name=None</em>, <em class="sig-param">shape=None</em>, <em class="sig-param">unit=None</em>, <em class="sig-param">dtype=None</em>, <em class="sig-param">prop_info=None</em>, <em class="sig-param">return_prop_info=False</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.load_atom_dump" title="Permalink to this definition">¶</a></dt>
<dd><p>Reads in a LAMMPS atomic dump file into a System.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>file-like object</em>) – The content, file path or file-like object containing the content to
read.</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – Allows the list of element symbols to be assigned during loading.</p></li>
<li><p><strong>lammps_units</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – The LAMMPS units option associated with the parameters.  Default value
is ‘metal’.</p></li>
<li><p><strong>prop_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The Atoms properties to generate.</p></li>
<li><p><strong>table_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The table column name(s) that correspond to each prop_name.  If
prop_name, table_name and prop_info are not given, prop_name and
table_name will be read in from data.</p></li>
<li><p><strong>shape</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The shape of each per-atom property.  If not given, will be taken from
standard LAMMPS parameter names, or left at () for direct
property-table conversion.</p></li>
<li><p><strong>unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – Lists the units for each prop_name as stored in the table.  For a
value of None, no conversion will be performed for that property.  For
a value of ‘scaled’, the corresponding table values will be taken in
box-scaled units.  If not given, all unit values will be set to None
(i.e. no conversions).</p></li>
<li><p><strong>dtype</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – Allows for the data type of each property to be explicitly given.
Values of None will infer the data type from the corresponding
property values.  If not given, all values will be None.</p></li>
<li><p><strong>prop_info</strong> (<em>list of dict</em><em>, </em><em>optional</em>) – Structured form of property conversion parameters, in which each
dictionary in the list corresponds to a single atoms property.  Each
dictionary must have a ‘prop_name’ field, and can optionally have
‘table_name’, ‘shape’, ‘unit’, and ‘dtype’ fields.</p></li>
<li><p><strong>return_prop_info</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Flag indicating if the full prop_info is to be returned.  Default value
is False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>system</strong> (<em>atomman.System</em>) – The generated system.</p></li>
<li><p><strong>prop_info</strong> (<em>list of dict</em>) – The full prop_info detailing the property-table conversion. Returned
if return_prop_info is True.</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.load_cif">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">load_cif</code><span class="sig-paren">(</span><em class="sig-param">cif</em>, <em class="sig-param">symbols=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.load_cif" title="Permalink to this definition">¶</a></dt>
<dd><p>Reads in a CIF crystal file.  Requires diffpy.Structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>cif</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>file-like object</em>) – The cif content to read.</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – Allows the list of element symbols to be assigned during loading.
Useful if the symbols for the model differ from the standard element
tags.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><strong>system</strong> – An atomman representation of a system.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.load_crystal">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">load_crystal</code><span class="sig-paren">(</span><em class="sig-param">name=None</em>, <em class="sig-param">key=None</em>, <em class="sig-param">method='dynamic'</em>, <em class="sig-param">standing='good'</em>, <em class="sig-param">family=None</em>, <em class="sig-param">parent_key=None</em>, <em class="sig-param">potential=None</em>, <em class="sig-param">potential_LAMMPS_id=None</em>, <em class="sig-param">potential_LAMMPS_key=None</em>, <em class="sig-param">potential_id=None</em>, <em class="sig-param">potential_key=None</em>, <em class="sig-param">symbols=None</em>, <em class="sig-param">natoms=None</em>, <em class="sig-param">natypes=None</em>, <em class="sig-param">prompt=True</em>, <em class="sig-param">refresh_cache=False</em>, <em class="sig-param">verbose=False</em>, <em class="sig-param">database=None</em>, <em class="sig-param">local=False</em>, <em class="sig-param">remote=True</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.load_crystal" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads a potential-dependent relaxed crystal record from the library.  If
multiple matches are found based on inputs a selection menu will appear.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – The record name(s) to parse by.  For relaxed crystal records, the
names should correspond to the key.</p></li>
<li><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – UUID4 key(s) to search for.  Each entry has a unique random-generated
UUID4 key.</p></li>
<li><p><strong>method</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.9)"><em>None</em></a><em>, </em><em>optional</em>) – The relaxation method used.  Allowed values are dynamic, static and box.
Default value is dynamic (the most rigorous relaxation method).  All
will be loaded if set to None.</p></li>
<li><p><strong>standing</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.9)"><em>None</em></a><em>, </em><em>optional</em>) – “good” records are the unique crystals found with the most rigorous
relaxation, and with known prototypes over DFT structures.  “bad” are
records filtered out, usually for being duplicates.  Default value is
“good”.  All will be loaded if set to None.</p></li>
<li><p><strong>family</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>atomman.library.CrystalPrototype</em><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The crystal family associated with the relaxed crystal - either crystal
prototype name or MP/OQMD database entry name.</p></li>
<li><p><strong>parent_key</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The UUID4 key(s) assigned to the calculation that the record is based
on.</p></li>
<li><p><strong>potential</strong> (<em>atomman.lammps.Potential</em><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – A loaded LAMMPS potential object to limit the search by.</p></li>
<li><p><strong>potential_LAMMPS_id</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The id for a LAMMPS implemented potential to limit the search by.</p></li>
<li><p><strong>potential_LAMMPS_key</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The UUID4 for a LAMMPS implemented potential to limit the search by.</p></li>
<li><p><strong>potential_id</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The id for a potential to limit the search by.</p></li>
<li><p><strong>potential_key</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The UUID4 for a potential to limit the search by.</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – Element symbols in the crystal to limit the search by.</p></li>
<li><p><strong>natypes</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The number of unique element model symbols in the crystal to limit
the search by.</p></li>
<li><p><strong>natoms</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The number of unique atoms in the crystal’s unit cell to limit the
search by.</p></li>
<li><p><strong>database</strong> (<a class="reference internal" href="atomman.library.Database.html#atomman.library.Database" title="atomman.library.Database"><em>atomman.library.Database</em></a><em>, </em><em>optional</em>) – A pre-defined Database object to use.  If not given, will initialize
a new Database object.  Passing in a database can save time if multiple
calls are made for the same record type.</p></li>
<li><p><strong>local</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Indicates if the Database object is to look for local records.  Default
is True.  Ignored if database is given.</p></li>
<li><p><strong>remote</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Indicates if the Database object is to look for remote records.  Default
is True.  Ignored if database is given.</p></li>
<li><p><strong>prompt</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a>) – If prompt=True (default) then a screen input will ask for a selection
if multiple matching potentials are found.  If prompt=False, then an
error will be thrown if multiple matches are found.</p></li>
<li><p><strong>refresh_cache</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If the local database is of style “local”, indicates if the metadata
cache file is to be refreshed.  If False,
metadata for new records will be added but the old record metadata
fields will not be updated.  If True, then the metadata for all
records will be regenerated, which is needed to update the metadata
for modified records.</p></li>
<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True, info messages will be printed during operations.  Default
value is False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><strong>system</strong> – The system object generated from the relaxed crystal.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.load_lammps_potential">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">load_lammps_potential</code><span class="sig-paren">(</span><em class="sig-param">name=None</em>, <em class="sig-param">key=None</em>, <em class="sig-param">id=None</em>, <em class="sig-param">potid=None</em>, <em class="sig-param">potkey=None</em>, <em class="sig-param">units=None</em>, <em class="sig-param">atom_style=None</em>, <em class="sig-param">pair_style=None</em>, <em class="sig-param">status='active'</em>, <em class="sig-param">symbols=None</em>, <em class="sig-param">elements=None</em>, <em class="sig-param">pot_dir_style=None</em>, <em class="sig-param">kim_models=None</em>, <em class="sig-param">kim_api_directory=None</em>, <em class="sig-param">kim_models_file=None</em>, <em class="sig-param">local=None</em>, <em class="sig-param">remote=None</em>, <em class="sig-param">database=None</em>, <em class="sig-param">getfiles=False</em>, <em class="sig-param">prompt=True</em>, <em class="sig-param">verbose=False</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.load_lammps_potential" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads a LAMMPS potential from the NIST Interatomic Potentials Repository
or from a local copy of the repository.  Will issue a prompt if
multiple LAMMPS potentials match the parameters given.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – The record name(s) to parse by.  For potential records, the names
should correspond to the id with a prefix of “potentials.” added to it.</p></li>
<li><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – The unique UUID4 record key(s) to parse by.</p></li>
<li><p><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – The unique record id(s) labeling the records to parse by.</p></li>
<li><p><strong>potid</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – The unique UUID4 record key(s) for the associated potential records to
parse by.</p></li>
<li><p><strong>potkey</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – The unique record id(s) labeling the associated potential records to
parse by.</p></li>
<li><p><strong>units</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – LAMMPS units option(s) to parse by.</p></li>
<li><p><strong>atom_style</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – LAMMPS pair_style(s) to parse by.</p></li>
<li><p><strong>pair_style</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – LAMMPS pair_style(s) to parse by.</p></li>
<li><p><strong>status</strong> (<a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.9)"><em>None</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – Limits the search by the status of the LAMMPS implementations:
“active”, “superseded” and/or “retracted”.  By default, only active
implementations are returned.  Giving a value of None will return
implementations of all statuses.</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – Model symbol(s) to parse by.  Typically correspond to elements for
atomic potential models.</p></li>
<li><p><strong>elements</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – Element(s) in the model to parse by.</p></li>
<li><p><strong>pot_dir_style</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – Specifies how the pot_dir values will be set for the retrieved LAMMPS
potentials.  Allowed values are ‘working’, ‘id’, and ‘local’.
‘working’ will set all pot_dir = ‘’, meaning parameter files
are expected in the working directory when the potential is accessed.
‘id’ sets the pot_dir values to match the potential’s id.
‘local’ sets the pot_dir values to the corresponding local database
paths where the files are expected to be found.  Default value is
controlled by settings.</p></li>
<li><p><strong>kim_models</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – A list of full KIM model ids to build LAMMPS potentials for.</p></li>
<li><p><strong>kim_api_directory</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – The path to the directory containing a kim-api-collections-management
executable to use to identify which KIM models are installed.</p></li>
<li><p><strong>kim_models_file</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – The path to a file containing a list of full KIM model ids to build
LAMMPS potentials for.</p></li>
<li><p><strong>local</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Indicates if the local location is to be searched.  Default value
matches the value set when the database was initialized.</p></li>
<li><p><strong>remote</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Indicates if the remote location is to be searched.  Default value
matches the value set when the database was initialized.</p></li>
<li><p><strong>database</strong> (<em>potentials.Database</em><em>, </em><em>optional</em>) – Allows for a previously defined Database object to be used to find
the potential.  If not given, a new Database object will be used with
the default local and remote interaction settings.</p></li>
<li><p><strong>getfiles</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True, then the parameter files for the matching potentials
will also be copied/downloaded to the potential directory.</p></li>
<li><p><strong>prompt</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a>) – If prompt=True (default) then a screen input will ask for a selection
if multiple matching potentials are found.  If prompt=False, then an
error will be thrown if multiple matches are found.</p></li>
<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True, info messages will be printed during operations.  Default
value is False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The potential object to use.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>potentials.record.PotentialLAMMPS</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If no matching LAMMPS potentials are found.</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.load_poscar">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">load_poscar</code><span class="sig-paren">(</span><em class="sig-param">poscar</em>, <em class="sig-param">symbols=None</em>, <em class="sig-param">prop={}</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.load_poscar" title="Permalink to this definition">¶</a></dt>
<dd><p>Reads a poscar-style coordination file for a system.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>poscar</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>file-like object</em>) – The POSCAR content to read</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – Allows the list of element symbols to be assigned during loading.
Useful if the symbols for the model differ from the standard element
tags or if the poscar file has no elemental information.</p></li>
<li><p><strong>prop</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a><em>, </em><em>optional</em>) – Dictionary containing any extra per-atom properties to include.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><strong>system</strong> – The system object associated with the poscar file.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.load_prototype">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">load_prototype</code><span class="sig-paren">(</span><em class="sig-param">name=None</em>, <em class="sig-param">id=None</em>, <em class="sig-param">key=None</em>, <em class="sig-param">commonname=None</em>, <em class="sig-param">prototype=None</em>, <em class="sig-param">pearson=None</em>, <em class="sig-param">strukturbericht=None</em>, <em class="sig-param">sg_number=None</em>, <em class="sig-param">sg_hm=None</em>, <em class="sig-param">sg_schoenflies=None</em>, <em class="sig-param">a=None</em>, <em class="sig-param">b=None</em>, <em class="sig-param">c=None</em>, <em class="sig-param">alpha=None</em>, <em class="sig-param">beta=None</em>, <em class="sig-param">gamma=None</em>, <em class="sig-param">symbols=None</em>, <em class="sig-param">database=None</em>, <em class="sig-param">local=True</em>, <em class="sig-param">remote=True</em>, <em class="sig-param">prompt=True</em>, <em class="sig-param">refresh_cache=False</em>, <em class="sig-param">verbose=False</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.load_prototype" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads a crystal prototype record from the library. If multiple matches
are found based on inputs a selection menu will appear.</p>
<dl class="simple">
<dt>name<span class="classifier">str or list, optional.</span></dt><dd><p>Record names to search for.  These should be the same values as id.</p>
</dd>
<dt>id<span class="classifier">str or list, optional</span></dt><dd><p>Prototype ID(s) to search for.  These are unique identifiers for each
prototype based on comm.</p>
</dd>
<dt>key<span class="classifier">str or list, optional</span></dt><dd><p>UUID4 key(s) to search for.  Each entry has a unique random-generated
UUID4 key.</p>
</dd>
<dt>commonname<span class="classifier">str or list, optional</span></dt><dd><p>Common name(s) to limit the search by.</p>
</dd>
<dt>prototype<span class="classifier">str or list, optional</span></dt><dd><p>Prototype identifying composition(s) to limit the search by.</p>
</dd>
<dt>pearson<span class="classifier">str or list, optional</span></dt><dd><p>The Pearson symbol(s) to limit the search by.</p>
</dd>
<dt>strukturbericht<span class="classifier">str or list, optional</span></dt><dd><p>The strukturbericht identifier(s) to limit the search by.</p>
</dd>
<dt>sg_number<span class="classifier">int or list, optional</span></dt><dd><p>The space group number(s) to limit the search by.</p>
</dd>
<dt>sg_hm<span class="classifier">str or list, optional</span></dt><dd><p>The space group Hermann-Maguin identifier(s) to limit the search by.</p>
</dd>
<dt>sg_schoenflies<span class="classifier">str or list, optional</span></dt><dd><p>The space group Schoenflies identifier(s) to limit the search by.</p>
</dd>
<dt>a<span class="classifier">float, optional</span></dt><dd><p>The a lattice parameter to scale the prototype by. Can only be given
if it is a unique lattice parameter for the prototype’s crystal family,
and if all other unique lattice parameters are given.</p>
</dd>
<dt>b<span class="classifier">float, optional</span></dt><dd><p>The b lattice parameter to scale the prototype by. Can only be given
if it is a unique lattice parameter for the prototype’s crystal family,
and if all other unique lattice parameters are given.</p>
</dd>
<dt>c<span class="classifier">float, optional</span></dt><dd><p>The c lattice parameter to scale the prototype by. Can only be given
if it is a unique lattice parameter for the prototype’s crystal family,
and if all other unique lattice parameters are given.</p>
</dd>
<dt>alpha<span class="classifier">float, optional</span></dt><dd><p>The alpha lattice angle to scale the prototype by. Can only be given
if it is a unique lattice parameter for the prototype’s crystal family,
and if all other unique lattice parameters are given.</p>
</dd>
<dt>beta<span class="classifier">float, optional</span></dt><dd><p>The beta lattice angle to scale the prototype by. Can only be given
if it is a unique lattice parameter for the prototype’s crystal family,
and if all other unique lattice parameters are given.</p>
</dd>
<dt>gamma<span class="classifier">gamma, optional</span></dt><dd><p>The alpha lattice angle to scale the prototype by. Can only be given
if it is a unique lattice parameter for the prototype’s crystal family,
and if all other unique lattice parameters are given.</p>
</dd>
<dt>symbols<span class="classifier">tuple, optional</span></dt><dd><p>Allows the list of element symbols to be assigned during loading.</p>
</dd>
<dt>database<span class="classifier">atomman.library.Database, optional</span></dt><dd><p>A pre-defined Database object to use.  If not given, will initialize
a new Database object.  Passing in a database can save time if multiple
calls are made for the same record type.</p>
</dd>
<dt>local<span class="classifier">bool, optional</span></dt><dd><p>Indicates if the Database object is to look for local records.  Default
is True.  Ignored if database is given.</p>
</dd>
<dt>remote<span class="classifier">bool, optional</span></dt><dd><p>Indicates if the Database object is to look for remote records.  Default
is True.  Ignored if database is given.</p>
</dd>
<dt>prompt<span class="classifier">bool, optional</span></dt><dd><p>If prompt=True (default) then a screen input will ask for a selection
if multiple matching potentials are found.  If prompt=False, then an
error will be thrown if multiple matches are found.</p>
</dd>
<dt>refresh_cache<span class="classifier">bool, optional</span></dt><dd><p>If the local database is of style “local”, indicates if the metadata
cache file is to be refreshed.  If False,
metadata for new records will be added but the old record metadata
fields will not be updated.  If True, then the metadata for all
records will be regenerated, which is needed to update the metadata
for modified records.</p>
</dd>
<dt>verbose<span class="classifier">bool, optional</span></dt><dd><p>If True, info messages will be printed during operations.  Default
value is False.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p><strong>system</strong> – The system object generated from the crystal prototype.</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.load_pymatgen_Structure">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">load_pymatgen_Structure</code><span class="sig-paren">(</span><em class="sig-param">structure</em>, <em class="sig-param">symbols=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.load_pymatgen_Structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Convert a pymatgen.Structure into an atomman.System.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<em>pymatgen.Structure</em>) – A pymatgen representation of a structure.</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – Allows the list of element symbols to be assigned during loading.
Useful if the symbols for the model differ from the standard element
tags.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><strong>system</strong> – A atomman representation of a system.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.load_system_model">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">load_system_model</code><span class="sig-paren">(</span><em class="sig-param">model</em>, <em class="sig-param">symbols=None</em>, <em class="sig-param">key='atomic-system'</em>, <em class="sig-param">index=0</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.load_system_model" title="Permalink to this definition">¶</a></dt>
<dd><p>Read in a data model containing a crystal structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>file-like object</em><em> or </em><em>DataModelDict</em>) – The data model to read.</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – Allows the list of element symbols to be assigned during loading.</p></li>
<li><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The key identifying the root element for the system definition.
Default value is ‘atomic-system’.</p></li>
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional.</em>) – If the full model has multiple key entries, the index specifies which
to access.  Default value is 0 (first, or only entry).</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><strong>system</strong> – The system object associated with the data model.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.load_table">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">load_table</code><span class="sig-paren">(</span><em class="sig-param">table</em>, <em class="sig-param">box</em>, <em class="sig-param">symbols=None</em>, <em class="sig-param">system=None</em>, <em class="sig-param">prop_name=None</em>, <em class="sig-param">table_name=None</em>, <em class="sig-param">shape=None</em>, <em class="sig-param">unit=None</em>, <em class="sig-param">dtype=None</em>, <em class="sig-param">prop_info=None</em>, <em class="sig-param">skiprows=None</em>, <em class="sig-param">nrows=None</em>, <em class="sig-param">comment=None</em>, <em class="sig-param">usecols=None</em>, <em class="sig-param">header='infer'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.load_table" title="Permalink to this definition">¶</a></dt>
<dd><p>Reads in tabular data into atomic properties.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>table</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>file-like object</em>) – The table content, file path or file-like object containing the
content to read.</p></li>
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – The atomic box to use when generating a System around the data.</p></li>
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – Allows the list of element symbols to be assigned during loading.</p></li>
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a><em>, </em><em>optional</em>) – The atomic system to load the values to.  If not given, a new system
will be constructed.</p></li>
<li><p><strong>prop_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The Atoms properties to generate.  Must be given if prop_info is not.</p></li>
<li><p><strong>table_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The table column name(s) that correspond to each prop_name.  If not
given, the table_name values will be based on the prop_name values.</p></li>
<li><p><strong>shape</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – The shape of each per-atom property.  If not given, will be inferred
from the length of each table_name value.</p></li>
<li><p><strong>unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – Lists the units for each prop_name as stored in the table.  For a
value of None, no conversion will be performed for that property.  For
a value of ‘scaled’, the corresponding table values will be taken in
box-scaled units.  If not given, all unit values will be set to None
(i.e. no conversions).</p></li>
<li><p><strong>dtype</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em>, </em><em>optional</em>) – Allows for the data type of each property to be explicitly given.
Values of None will infer the data type from the corresponding
property values.  If not given, all values will be None.</p></li>
<li><p><strong>prop_info</strong> (<em>list of dict</em><em>, </em><em>optional</em>) – Structured form of property conversion parameters, in which each
dictionary in the list corresponds to a single atoms property.  Each
dictionary must have a ‘prop_name’ field, and can optionally have
‘table_name’, ‘shape’, ‘unit’, and ‘dtype’ fields.</p></li>
<li><p><strong>skiprows</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – Number of rows to skip before reading the data.</p></li>
<li><p><strong>usecols</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – Which columns are to be used. Will be passed to pandas.read_csv() usecols
option.</p></li>
<li><p><strong>nrows</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – Number of rows of data to read.</p></li>
<li><p><strong>comment</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – Specifies a character which indicates all text on a given line after
is to be considered to be a comment and ignored by parser. This is
often ‘#’.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The generated system.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.nlist">
<code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">nlist</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomman.nlist" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates a neighbor list for all atoms in a System taking periodic
boundaries into account.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – The system to calculate the neighbor list for.</p></li>
<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a>) – Radial cutoff distance for identifying neighbors.</p></li>
<li><p><strong>initialsize</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – The number of neighbor positions to initially assign to each atom.
Default value is 20.</p></li>
<li><p><strong>deltasize</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – Specifies the number of extra neighbor positions to allow each atom
when the number of neighbors exceeds the underlying array size.
Default value is 10.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Array listing number of neighbors and neighbor ids for each atom in
System.  First term in each row is the atom’s coordination number, c.
The next c values are the atom’s neighbor ids.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>numpy.ndarray of int</p>
</dd>
</dl>
</dd></dl>

</div>
</div>


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  <h3><a href="index.html">Table of Contents</a></h3>
  <ul>
<li><a class="reference internal" href="#">atomman package</a><ul>
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